I suspect Cryptic will ultimately follow something similar to Turbine's model of releasing "adventure packs". For example in DDO, Turbine generally releases 4 adventure packs every year. Subscribers and lifetime members automatically get all adventure packs unlocked so they don't have to pay for these adventure packs.
For F2P players, they generally get one adventure pack for free every year (typically in March, when the number of players are at an all-year low). The remaining three adventure packs, generally released just prior to major school breaks and major holidays, are locked and F2P players have to pay to get these adventure packs unlocked.
CO (Cryptic's other MMORPG) used to sell adventure packs but after the first two they started making them free.
The situation has changed. The majority of the players are now F2P players with little investment in STO and extremely short attention span. What's worse, they may not even be a fan of Star Trek, so ships like the Ambassador class which have sentimental value to us trek fans are simply another ship.
What these f2p players "want" is to have an interesting fun adventure, and the universal MMO constant of desiring better equipment. So it makes sense for Cryptic to start producing C-Store FEs and ships.